From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp11.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms0.migadu.com with LMTPS id qIIDCSbZzmHmfQEAgWs5BA (envelope-from ) for ; Fri, 31 Dec 2021 11:19:18 +0100 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp11.migadu.com with LMTPS id AMl2BibZzmFrLAEA9RJhRA (envelope-from ) for ; Fri, 31 Dec 2021 11:19:18 +0100 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 94DF32FFD0 for ; Fri, 31 Dec 2021 11:19:17 +0100 (CET) Received: from localhost ([::1]:36434 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1n3F0G-0004Qi-Ri for larch@yhetil.org; Fri, 31 Dec 2021 05:19:16 -0500 Received: from eggs.gnu.org ([209.51.188.92]:46716) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1n3F02-0004QC-Hc for bug-guix@gnu.org; Fri, 31 Dec 2021 05:19:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:43585) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1n3F02-0007qI-6Q for bug-guix@gnu.org; Fri, 31 Dec 2021 05:19:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1n3F02-0006Y5-3L for bug-guix@gnu.org; Fri, 31 Dec 2021 05:19:02 -0500 X-Loop: help-debbugs@gnu.org Subject: bug#52906: python-biopython conflicts with python-numpy Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Fri, 31 Dec 2021 10:19:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 52906 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: zimoun X-Debbugs-Original-Cc: debbugs-submit@debbugs.gnu.org, 52906@debbugs.gnu.org Received: via spool by 52906-submit@debbugs.gnu.org id=B52906.164094589125062 (code B ref 52906); Fri, 31 Dec 2021 10:19:02 +0000 Received: (at 52906) by debbugs.gnu.org; 31 Dec 2021 10:18:11 +0000 Received: from localhost ([127.0.0.1]:55126 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n3EzC-0006W9-LG for submit@debbugs.gnu.org; Fri, 31 Dec 2021 05:18:10 -0500 Received: from sender3-of-o51.zoho.com ([136.143.184.51]:21192) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1n3EzA-0006Vt-Vm; Fri, 31 Dec 2021 05:18:09 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1640945887; cv=none; d=zohomail.com; s=zohoarc; b=mzL4y4XsTVxtTlMF41bFETTfxDC+TkWPJsSXgw5gXHmRtABkrRm6gjxN7h4EGhQ7bLmbHQiRLaxnUbezJIBF/IYBqt/qJoWt1KnbHAvavPxa5CV1IMP7zzq+w6kpyVOJpHu35/cvK1m2We/p46cJXgTmjtYJ3BizKEe4+MSMYII= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1640945887; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=6kffbOQVpNk00RivrUNgGAcAKXt+pTHAcdNXAzmJgew=; b=OZklOi3k0tY3WyJ0ZipMoxtgO4stfQin2FuRPgmBsmo37lqPrw2qBm1Rr2NeOxos9xlZxxJZZkatmpM8ivMzXRz5PKmkkcY8/YF270VDqwkbCvhhYx6mQTOad2s6c+5ZPrAcbDSkyoZ0C4wCjIRqkyQpbhELhHiNitu4LeDYV2Q= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1640945887; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:Date:In-reply-to:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=6kffbOQVpNk00RivrUNgGAcAKXt+pTHAcdNXAzmJgew=; b=gSp7NuEE3M6DP4ETCUHV2aeNj8+W3GLntmkXOsV+zbMgsJEeI+XBV1EE952ryxli 0pqakaPwViq3Qy6VBorye3Kq9QgixJ/BAtUo7YeLYaLSlt1FRXBV8gFrFKhCE4tA2Ef PacuOyjYYTJE/Ord6/DvlJbVWbho+F8UX+YWX3wc= Received: from localhost (p54ad4eae.dip0.t-ipconnect.de [84.173.78.174]) by mx.zohomail.com with SMTPS id 1640945885129657.1187773466229; Fri, 31 Dec 2021 02:18:05 -0800 (PST) References: <86o84xpzhv.fsf@gmail.com> User-agent: mu4e 1.6.10; emacs 27.2 From: Ricardo Wurmus Date: Fri, 31 Dec 2021 11:14:22 +0100 In-reply-to: <86o84xpzhv.fsf@gmail.com> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Message-ID: <877dblgjs5.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: 52906@debbugs.gnu.org Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN X-Migadu-Country: US ARC-Message-Signature: i=2; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1640945957; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding:resent-cc: resent-from:resent-sender:resent-message-id:in-reply-to:in-reply-to: references:references:list-id:list-help:list-unsubscribe: list-subscribe:list-post:dkim-signature; bh=6kffbOQVpNk00RivrUNgGAcAKXt+pTHAcdNXAzmJgew=; b=M4MnRfOfamLqPHELZ9HEk5O9lMzhrnp83lU5MvFPiSyj+n+kBPbbYHnAAMbkgCETC2/8av Yr2foad7n8L665uwG9CNQAALNXF61joSJhWOv8EYMONXIXzdh1vWO9WO/5SthNeZdIHAcN OcEaiDay37/RF/tj1rkr8i/9GTgYIAcjg5SoGjyDp0Wyuc4kARAaBeEYqLaIU0+o21KB2r h6CzVTqWyMANWzOJ78w5B36FUwfPwLczT5eLfVReqFhSFP2WYWKawGMHozOjklv+rNYNM2 8LzjW/VjQPYmOyp8JcWbSadnXNmApU3fLP9DSJxJVtyi/DCoGda69D9M5qQ2cw== ARC-Seal: i=2; s=key1; d=yhetil.org; t=1640945957; a=rsa-sha256; cv=fail; b=sgd4hZHLyM02OFQG96hCAaOqQiF2PkyM2a8iCMVFbbCBGKnRDdb/t44tIZPQHXtec57zhI lMWzJoCYfnzrxTp/O5xj+zSjfS0F8VESEIMGtAfhNhEoG4LihuqX2z1Ca7YUxVkzO+EdUd Xz+7Mo5x+OodxwkLKt0AwU15vO1b/K1J5LgpphBfh/csLxAl1XMU1FP4h9/xv1pJuLh9dL JfhTmztx6oZZ7PpyZCi4Sz8arE10jLS32BPQHmyS3vDKEBZbxvT+/NUjsfhp1VvcXL+yV6 nXyeFDkabPW64E9Km+NG7MDZAxukBpB1UK0oicq8b4sqorA34zEf2YcRQbJCkQ== ARC-Authentication-Results: i=2; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=elephly.net header.s=zoho header.b=gSp7NuEE; arc=reject ("signature check failed: fail, {[1] = sig:zohomail.com:reject}"); dmarc=none; spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: -1.08 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=elephly.net header.s=zoho header.b=gSp7NuEE; arc=reject ("signature check failed: fail, {[1] = sig:zohomail.com:reject}"); dmarc=none; spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 94DF32FFD0 X-Spam-Score: -1.08 X-Migadu-Scanner: scn0.migadu.com X-TUID: yqmzsGx52WuQ zimoun writes: > Hi, > > Using 7022eb6, the package =E2=80=99python-biopython=E2=80=99 propagates > =E2=80=99python-numpy=E2=80=99, i.e., python-numpy@1.20. Back then we reverted to numpy 1.20.x as the default because of numba, which did not work with 1.21. I=E2=80=99m now upgrading numba (and llvmlit= e) to a more recent release candidate, which should bring compatibility with numpy 1.21. If that works we=E2=80=99ll make python-numpy-next the new python-numpy. Your patch is an acceptable workaround. Arguably this should have been done when I made numpy 1.20 the default on the core-updates-frozen branch. I=E2=80=99ll apply your patch later today unless the switch to num= py 1.21 as the default is successful. --=20 Ricardo